Hello Vipin, Good to see this. just a quick question, does your interface has the functionality to define groups (say normal or control) for replicates/samples, as the way we define in edgeR/DESeq R script.
Carlos, I think BAM input would be okay as it can be connected with tophat in the workflow. Let me know your suggestions. Praveen. -----Original Message----- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Carlos Borroto Sent: Tuesday, March 27, 2012 12:44 AM To: Vipin TS Cc: Galaxy Dev Subject: Re: [galaxy-dev] R scripts for DESeq Thanks for the update. I wonder if when you had the time to upload your script to the toolshed, you could use a different name from just plain DESeq to avoid confusion. A researcher might expect a DESeq tool to use a read count table and not BAM files as input. Kind regards, Carlos On Mon, Mar 26, 2012 at 2:49 PM, Vipin TS <vipin...@gmail.com> wrote: > Hi Carlos, > Currently I am in a transition period, and I didn't get much time to look on > the same, Sorry for the delay. > > For getting the read count, we wrote script and which is wrapped in Deseq > main program. > > regards, > --Vipin T S > > > > On 26 March 2012 14:01, Carlos Borroto <carlos.borr...@gmail.com> wrote: >> >> Hi Vipin, >> >> I was wondering if there is any progress on getting your DESeq wrapper >> into the Tool Shed? I'm also highly interested on using DESeq inside >> Galaxy. >> >> Also, what you use for generating the read counts for DESeq? Do you >> produce these counts inside Galaxy? >> >> Thanks, >> Carlos >> >> On Thu, Feb 23, 2012 at 4:46 AM, Vipin TS <vipin...@gmail.com> wrote: >> > Hi Chris, >> > >> > We are running DESEQ_VERSION 1.6.0 at our instance >> > http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq >> > >> > thanks, >> > --Vipin T S >> > >> > >> > >> >> Which version of DESeq does this tool use? >> >> >> >> Note that there are significant differences between DESeq 1.4 (the >> >> version >> >> described in the paper) and 1.6.x (current release). The differences >> >> are >> >> both in functionality and results. >> >> Regards, >> >> >> >> >> >> Chris >> >> >> >> On 23/02/2012 02:27, "Greg Von Kuster" <g...@bx.psu.edu> wrote: >> >> >> >> >Lisa, >> >> > >> >> >In case you aren't aware, you can set your user preferences for your >> >> >account in the tool shed to receive an email message when a new >> >> >repository's first upload occurs. This would keep you from having to >> >> >check the tool shed. Go to User -> Preferences -> Manage >> >> > your email alerts and you'll see the following setting. >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> >On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote: >> >> > >> >> >> Hi Vipin, >> >> >> That is a wonderful news and I am eager to see it in tool shed. I am >> >> >> going to check tool shed frequently these days to get it asap. >> >> >> >> >> >> Thanks >> >> >> Lisa >> >> >> >> >> >> On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS <vipin...@gmail.com> >> >> >> wrote: >> >> >>> Hi, >> >> >>> >> >> >>> We have the recent release version of DESeq at our Galaxy instance, >> >> >>> >> >> >>> http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq >> >> >>> >> >> >>> I will add the Galaxy wrapper for DESeq in community tool shed in >> >> >>> few >> >> >>>days. >> >> >>> >> >> >>> regards, >> >> >>> --Vipin >> >> >>> >> >> >>>> Hi Lisa, >> >> >>>> >> >> >>>> I am going to send your question over to the galaxy-...@bx.psu.edu >> >> >>>>mailing >> >> >>>> list so that the development community can offer feedback. >> >> >>>> >> >> >>>> >> >> >> >> > >> >> > > >http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clou >> >> >d_instance.2C_or_development_thread >> >> >> >> > >> >> > > ><http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-clo >> >> >ud_instance.2C_or_development_thread> >> >> >>>> >> >> >>>> Th galaxy-user list is primarily for tool/data usage on the Galaxy >> >> >>>>public >> >> >>>> server. >> >> >>>> http://wiki.g2.bx.psu.edu/Mailing%20Lists >> >> >>>> >> >> >>>> Thanks, >> >> >>>> >> >> >>>> Jen >> >> >>>> Galaxy team >> >> >>>> >> >> >>>> >> >> >>>> -------- Original Message -------- >> >> >>>> Subject: [galaxy-user] R scripts for DESeq >> >> >>>> Date: Tue, 21 Feb 2012 23:25:35 -0500 >> >> >>>> From: Liusong Yang <liusongyang2...@gmail.com> >> >> >>>> To: galaxy-u...@lists.bx.psu.edu >> >> >>>> >> >> >>>> Hello, >> >> >>>> >> >> >>>> I am planning to put DESeq into galaxy. I am a newcomer for both >> >> >>>> Galaxy and R. I have already read all of the related discussion in >> >> >>>> this group. I also noticed that there are r_wrapper.sh and >> >> >>>> DESeq.xml >> >> >>>> added into galaxy recently under the path of tools. >> >> >>>> >> >> >>>> These lines are from r_wrapper.sh. >> >> >>>> >> >> >>>> ### Run R providing the R script in $1 as standard input and >> >> >>>> passing >> >> >>>> ### the remaining arguments on the command line >> >> >>>> >> >> >>>> >> >> >>>> I guess this means we need to give the DESeq R script to the >> >> >>>> wrapper >> >> >>>> as standard input. My question is where or what is the DESeq R >> >> >>>> scripts? I installed R and DESeq package, but I can not fund >> >> >>>> anything >> >> >>>> like DESeq.R or something similar? I feel so confusing now. Any >> >> >>>> comments or suggestions would be absolutely appreciated! >> >> >>>> >> >> >>>> Thanks >> >> >>>> >> >> >>>> Lisa >> >> >>>> ___________________________________________________________ >> >> >>>> The Galaxy User list should be used for the discussion of >> >> >>>> Galaxy analysis and other features on the public server >> >> >>>> at usegalaxy.org. Please keep all replies on the list by >> >> >>>> using "reply all" in your mail client. 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To manage your subscriptions to this >> >> >> and other Galaxy lists, please use the interface at: >> >> >> >> >> >> http://lists.bx.psu.edu/ >> >> >> >> >> > >> >> > >> >> > >> >> >___________________________________________________________ >> >> >Please keep all replies on the list by using "reply all" >> >> >in your mail client. To manage your subscriptions to this >> >> >and other Galaxy lists, please use the interface at: >> >> > >> >> > http://lists.bx.psu.edu/ >> >> > >> >> >> >> >> >> The University of Dundee is a registered Scottish Charity, No: SC015096 >> >> >> >> >> >> ___________________________________________________________ >> >> Please keep all replies on the list by using "reply all" >> >> in your mail client. 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